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I work in Theoretical CS for context.

There is this problem A I've been working on for the past year and wrote and submitted a paper X 3 months ago on a new bound we proved for A. I just recently (literally 2 days ago) got the first round of feedback on the paper and it is extremely good. The reviewers mostly want minor changes and recommended acceptance.

However, in the last 3 month (since I submitted X), I continued working on the problem and broke that upper bound again (just a few weeks ago). I wrote another paper Y that uses a lot of the ideas from paper X, but of course with 1 major key new idea that broke the previous improved upper bound.

I am worried that if I submit Y, the reviewers will think that I got two ideas, and instead of just directly submitting the better Y directly, I decided to "break" things up into two papers instead.

Would this raise any eyebrows or am I overthinking this?

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Some people might think that and "salami publishing" can be a problem. But your options are limited. It would probably be a mistake to delay the submission of the second paper, lest someone else pick up on the idea. It would probably be a mistake to incorporate the new ideas into the first paper as it will require a new round of review with an uncertain outcome.

If an editor asks, just reassure them that the new ideas came as a result of completing the first paper. That is completely natural.

If the first paper stands on its own, as seems likely, then you really don't have a problem. Of course, the reviewers of the second might not agree that it is a sufficient advance over the first to warrant publication, but that is true in any case. Carry on.

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